Running Silent:

Moving Forward

…

An alternate ME3. Commander Shepard and her team are on the run from Cerberus and trying to make alliances before it's too late. In a galaxy with no reaper kill switch, how can they hope to defeat something so ancient and powerful? Their last hope is a desperate plan that may cost them everything. Shepard/Garrus, other side pairings.

…

Disclaimer: This author in no way profits from the writing of this story. All characters, dialogue, or other referenced material from the Mass Effect trilogy belong to Bioware.

…

Shepard stood in the doorway of the darkened lab, staring at the place Mordin used to work. It felt selfish to mourn one life when countless others were dying daily, but this one hit close to home.

These thoughts brought to mind the first Normandy and the others she had lost due to this war. For Shepard, the first loss of the war was Ashley. And following her, the twenty crewmen that lost their lives when the first Normandy was destroyed. There must be some way to honor these losses. There was no time for funerals, not while the war was ongoing, but there must be something she could do.

With this thought in mind, she slipped out of the lab and went towards the elevator, heading down to the crew deck. She needed to check on Maelon.

She found the salarian staring out the windows of the observation room. "Are you okay?" she asked quietly.

"No," came the quiet answer. "Maybe. I don't know."

His eyes were steady on the void of space as she came up beside him. "It should have been me," he insisted. "I messed up so many times. I hurt so many people to get to this point. Why didn't he let me go up instead?"

"I can't answer that for sure," Shepard said, shaking her head. "Maybe he felt he had something to atone for. He spent so many years working on the genophage, arguing that it was right. His change of heart could have come with some very heavy guilt."

"I'm sure it could have," Maelon agreed. "Mine did."

"He was old," Shepard added. "He didn't have much time left to make up for past mistakes. But you do. He saw something in you. The potential for something good. I think he wanted to make sure you had the chance to realize it."

Maelon sighed. "I don't know if he was right. But maybe I can try to be the person he thought I could be." He finally looked at her, a small smile curving his lips despite the bleak look in his eyes. "Thank you, Commander."

She gave him a small smile back. "Don't let yourself drown in this, Maelon. Come see me if you need to talk." And she slipped back out the door, leaving him to his thoughts.

…

Shepard always felt relief in returning to her quarters. She had to be strong for so many people. Her crew was counting on her, not just to save the galaxy but to keep them moving forward. She didn't have to be cheerful, but she couldn't let them see her fear or uncertainty. And there was plenty of that going around. She sighed in relief as the door panels closed behind her.

"Commander," came the AI's voice a moment later.

"Yes, EDI?" she said tiredly. She supposed work wasn't quite finished for the day.

"Are you well, Shepard?" EDI asked, in a voice gentler than what Shepard was used to from the AI.

"Well enough," she said. "I have to be."

"It is right and natural to mourn." The AI cut right to the heart of the matter.

Shepard sat down heavily in the chair beside her bed. "That may be so, but we're also in the middle of a war. I need to stay strong for my team." Her lips curved into a half-smile. "You won't tell if I shed a few tears privately in my quarters, I hope."

"I will always keep your secrets, Commander."

"I trust you, EDI," Shepard assured her. "I was only teasing a little. Trying to lighten the mood." She paused. "Do you mourn Mordin like we do?"

"I honor his life and his sacrifice," the AI said quickly, but then added, "And I will miss his presence."

Shepard sighed. "So will I. But you didn't just call to check up on me, did you?"

"No, Shepard. I wanted to alert you that Harbinger was sighted in the Aralakh system not long after we left, as was Cerberus."

"They're both still hunting us?" Shepard asked.

"It appears so," said EDI.

Shepard sighed. "We'll have to be careful. Can't stay in any system too long. Is there anything else?"

"No, Commander," EDI said. "I will leave you to your thoughts now."

Shepard, who had no true desire to be alone with her thoughts, worked on her omni-tool until Garrus came up to bed. They took comfort in each other, trying to dull the pain of their losses. After making love, they lay together in silence for a while.

"I want to find a way to honor him," Shepard said. "Him and all the others. I know there's no time for funerals, but he deserves better than that."

Garrus ran his talons gently through her hair. "Maybe some kind of memorial or monument?" he suggested. "Like what you left on Alchera?"

Shepard looked thoughtful. "When I was young, they made me go back to Mindoir to open the memorial there. It had the names of everyone that died in the raid. Maybe we could have something like that here on the Normandy? To honor all the past crew who have died. Mordin, Ashley, and all the others."

Garrus nuzzled into her neck. "I think that's a wonderful idea. I'll talk to Miranda about making it happen."

Some of the tightness in Shepard's chest eased. "Thank you, Garrus."

…

The following day, Shepard found herself back in Mordin's lab. This time, the lights were on and a salarian was working. Shepard's heart leapt at the sight, but reality came to bear when Maelon turned around.

"I'm just cleaning up, Commander." He bustled around the room, placing items in cabinets and drawers. "We left it a bit of a mess before going down to Tuchanka."

"Thank you," she said, her throat tight. "Now that we've dispersed the cure, you don't need to remain with us, Maelon. Where would you like us to take you?"

He fidgeted. "I think I'd… I'd like to work on the war effort. Mordin said something about a project called Scythe? A weapon to defeat the reapers?"

She looked at him keenly, seeing the signs of worry and sleeplessness on him. "Are you sure, Maelon?"

He nodded, firm. "I'm sure. I want to do good in this galaxy. Like Mordin would have wanted."

A small smile grew on Shepard's face. "I understand. We can take you where you need to go."

…

Shepard made her way to the comm room where Liara's hologram was waiting. She looked more worried and careworn than the last time Shepard had seen her. Was this just worry about Project Pyrrhus or was it something more?

"What's happening, Liara?" she asked, stepping into the QEC.

Liara's troubled eyes met Shepard's. "I've discovered something that may help us. A hidden prothean archive, still mostly untapped."

"Alright," Shepard said, frowning, knowing there was more to this than Liara had said. "What's the catch?"

Liara took a deep breath. "It's on Thessia."

Shepard's eyes widened. "On Thessia?" Her mind reeled with the implications.

Her friend's eyes were pleading. "Hidden inside one of our protected heritage sites. The temple of Athame. I know how this must look, Shepard."

"I'm not sure you do, Liara," Shepard said slowly. "Hiding this from other species is against intergalactic law. Law the asari wrote! It could even go so far as to explain the stranglehold the asari have had over intergalactic politics for so long." She paced, mind racing with the possibilities.

Liara's brow creased in worry. "Shepard, please…"

Shepard waved a hand dismissively. "I know. More important things to worry about right now. Why is it mostly untapped? Why do you think we can get more use out of it than the asari have in the, oh… centuries since they discovered it?"

"So few people have access to this. It can't have been mined the way the publicly known archives have. As you know, it takes years, sometimes decades, to decode every little bit of information from a prothean archive, and that's with teams of people working them. But with the cipher…"

"You think the cipher can help us interpret the information more quickly?" Shepard asked.

Liara nodded firmly. "I do. If we can establish a neural link, like with the beacons, the data should rearrange itself to be easier understood. Then EDI can sort through it quicker than any organic could dream of."

Shepard sighed, running her fingers through her hair. "But should we even bother with this?"

"What do you mean?" Liara asked.

Shepard paced the room. "The protheans don't have the answers I need. They lost their war! Why should I divert to the archive instead of gathering things we know will help the war effort? Won't I be putting my crew in enough danger just setting down on Thessia right now?"

Liara's brow creased. "We don't know for sure if they have what you need, but much of their technology was more advanced than ours. If there's anything that could help with the Scythe or with Project Pyrrhus, it would be worth it."

"I know we need all the help we can get," Shepard said softly. "It's just… these homeworlds are dangerous, Liara. People are dying." Her voice shook slightly. "If I die down there, what will happen to the war?"

Liara was silent for a moment, watching Shepard sadly before speaking again. "Perhaps we can call in some extra help," she said finally, voice softened. "I can have a squad of my Shadow Broker troops sent down to secure the area as much as possible before you go in. I also have contact information for Samara. We will, more than likely, need her help to get into the temple."

Shepard shook her head. "I hope this is worth it."

"I hope so too. It was all I could to do even find out what they were hiding in the temple. This may be my government's most tightly held secret." She wrung her hands.

"Well, it would have to be," Shepard said back. "Think of what could happen if news of this got out."

"Shepard… I—"

"I know, Liara," Shepard interrupted, annoyance mingling with understanding. "I'll keep the secret for now. The last thing we need right now is resentment between our races. How did you even learn about this?"

Liara crossed her arms. "It wasn't through my Shadow Broker channels. It was…" She sighed. "My mother."

Shepard blinked. "Benezia?"

Liara nodded. "I've been going through the files she left for me. There's a great deal here, much of it purely personal. But not all." She paused, looking into the distance. "Before she joined with Saren, she was highly respected on Thessia. Involved with the government. That's how she must have learned about it. She couldn't write about it directly, but she left enough hints." Liara met her eyes. "She wanted me to find this, Shepard."

"And what's more," she continued. "Some of this was written after she joined Saren. It's—disjointed," Liara said uncomfortably. "But it's like she was beginning to understand what was coming. When she could break out of Sovereign's control, she understood how bad it could be. I think she was trying to help me."

Shepard let out a breath. "Alright, Liara," she agreed, despite her misgivings. "We'll check it out." Then she paused, a smile beginning to curve her lips. "You're coming with, right?"

The asari looked affronted. "As if I would ever miss this opportunity!"

Shepard's smile grew in spite of herself. "Just like old times."

…

It was three days later, when they were on the shuttle back from picking up a prothean obelisk from the Shrike Abyssal when Shepard's omni-tool buzzed with an incoming voice call.

"Hello, Commander," came a calm, soothing voice.

Shepard smiled. "Samara! Glad to see you're still kicking."

"I am fighting the reapers in my own way," she said. "The Shadow Broker's message said you needed my help."

The shuttle landed in the Normandy's docking bay and Shepard indicated for her team to go on ahead. "I need to get into the Temple of Athame on Thessia, without the interference of the asari government. It's important." She paced across the shuttle floor.

There was a long pause with only the sound of Shepard's footsteps echoing in the shuttle.

"What is it you seek, Shepard?" Samara finally replied. "You know I cannot aid you in doing anything dishonorable."

Shepard shook her head. "I'm not the dishonorable one in this situation. Inside the temple is a hidden prothean archive. The information contained within it may help us win the war."

"A secret archive?" Samara repeated, her voice as calm and level as ever.

"Yes, the asari government has kept it hidden since its discovery. It may go so far as to explain why asari have dominated our galaxy for so long." Shepard tried not to allow any anger to slip into her voice.

"I… see. I will help you in this endeavor. And when the war is over, I will ensure the archive's knowledge is spread throughout the galaxy."

Shepard smiled. "Thank you, Samara."

"I will contact you soon, Shepard. Once everything is arranged."

"We'll make preparations on our end until I hear from you. Shepard out."

…

In between smaller missions, Shepard moved ahead with preparations for dropping on Thessia. She had no intention of going in unprepared for what might await them. First were modifications to the shuttle. If something as large as the Normandy could be cloaked (or a dreadnought, as she'd seen the salarians do), there was no way they couldn't manage a cloak for the shuttle. She also had her engineers increasing the speed, shielding, and guns to better protect them.

The temple was in a highly populated area of Thessia, right in the center of Armali. They couldn't land the shuttle there without attracting a lot of reaper attention. If there was any way to minimize that and give them a chance of getting out in one piece, Shepard would take it.

The Normandy would remain away from the reapers surrounding Thessia, cloaking as soon as it came through the relay. Hopefully that would keep the reapers from alerting Harbinger to their presence. If not, well… she only hoped they'd have enough time to get out of the system.

And there was one more preparation she needed to make. Using the intercom, she asked Garrus to come up to her cabin. Waiting for him, she ran her fingers anxiously through her hair. This wasn't going to be an easy conversation.

It didn't take him long to come through the cabin door, a worried look on his face. "Hey, Shepard, what's going on?"

She led him over to the couches and sat down. "Garrus, I'm sure you have already guessed that you'll be going down to Thessia with me, once Samara makes the arrangements."

"Of course," he said immediately. "I've always got your six, Shepard."

"Right," she said, uncomfortable. "Well, I want you to be prepared to take over if necessary while we're down there. There's a chance that accessing the archive could put me… out of commission for a short while." She looked down at her hands, twining in her lap.

"Out of commission?" he asked, voice flanging with obvious concern. "What do you mean?"

She huffed a sigh. "You may not have known, since we didn't meet until afterwards, but… the beacon on Eden Prime knocked me out for fifteen hours."

"Fifteen hours?" he exclaimed, making her wince. "That's not comforting, Shepard." His blue eyes gazed worriedly at her.

"The beacon was damaged," she reminded him, reaching out a hand to cover his. "That's not supposed to happen, especially now that I have the cipher. But we need to be prepared for all contingencies. I'm not sure what the neural connection to this archive will do." Her gaze was firm, if apologetic.

"I'll be ready," he promised. "But I want to bring an additional squadmate. If you're knocked out, that's two people out of commission. You, and the person carrying you back to the shuttle."

"That makes sense," she agreed. "Do you have a request on who to bring?"

He shrugged. "Jacob's still feeling restless after healing from his injury. He's strong enough to help you out of there if need be."

Shepard nodded. "I'll let Jacob know. Thank you for being reasonable about this."

Garrus raised a brow plate in a wry expression. "Asking you not to do something insane has never worked so far. I've learned it's better to just be prepared." His expression turned serious. "Although, this time I really hope we don't need it."

"We probably won't," she reassured him. "I handled the beacon on Virmire just fine, if you recall. I just want to make sure we're ready for anything."

Garrus tugged on the hand he still held until Shepard was leaned up against his side. "I hope we are," he said, the worried tone in his voice still present.

Though Shepard didn't say so out loud, she couldn't help but share his misgivings.

…